When the Anti-Federalist League evolved into the UK Independence Party (UKIP), Mackinlay was appointed its founding treasurer[8] and Vice-Chairman. He stood again in Gillingham at the 1997 general election, receiving 590 votes.[9]

In July 1997, Sked resigned as UKIP leader, nominating Mackinlay as his successor.[10] Mackinlay decided that the only way to keep the party going was to rework its constitution and hold a leadership election. Mackinlay stood in the election against Michael Holmes[11] and Gerald Roberts. Holmes, with the backing of Nigel Farage, easily won and appointed Mackinlay as his deputy.[10]

Mackinlay remained active in UKIP, standing in Totnes at the 2001 general election, at which he received 6.1% of the vote,[12] then back again in Gillingham in 2005, where he polled 2.6%.[9] He also stood unsuccessfully in the 1994, 1999 and 2004 European elections.[13]

In 2010, he fell out with Kent Police over Special Constable David Craggs, who was advised that there would be no conflict with him standing for election to Medway Council but, after being elected as a councillor, was informed that he could not hold both roles.[16] In May 2011, Mackinlay was appointed a member of KentPolice Authority.[17]

In January 2016, the Labour Party unsuccessfully proposed an amendment in Parliament that would have required private landlords to make their homes "fit for human habitation". According to Parliament's register of interests, Mackinlay was one of 72 Conservative MPs who voted against the amendment who personally derived an income from renting out property. The Conservative Government had responded to the amendment that they believed homes should be fit for human habitation but did not want to pass the new law that would explicitly require it.[20]

In October 2017 he said "unemployed young people from Glasgow should get on their bikes and work with gorgeous EU women on farms in the south of England after Brexit." Labour MSP James Kelly responded that the comments were "abhorrent and offensive", while Jenny Gilruth MSP said that the comments were "sexist and patronising".[21]

In June 2018 it was reported that Mackinlay had been found to have twice breached parliament’s rules due to a potential financial interest, according to a decision by its standards watchdog. The MP had used his position to press for the reopening of an airport from which his company had planned to run low-cost flights. Mackinlay responded that he longer had plans for running flights from Manston Airport and that there 'was no suggestion he benefited financially from raising the matter in the Commons.'[22]

In the House of Commons he sits on the Committee on Exiting the European Union. He has previously sat on the Work and Pensions Select Committee and European Scrutiny Committee.[23][24]

Electoral spending criminal investigation following the 2015 General Election[edit]

In 2016–17, the United Kingdom general election, 2015 party spending investigation revealed that the Conservative Party had spent many thousands of pounds centrally on campaign buses to transport activists, and hotel accommodation for the activists, who went to campaign in marginal constituencies, including South Thanet. The expenditure on the buses was declared by the Conservative Party on its national declaration of "Campaign Spending", but in some cases the hotel accommodation was not declared at all as election spending when it should have been.
In addition, there is controversy about whether the expenditure, both on the buses and the accommodation, should have been declared on the declarations of expenditure for the constituency made by each candidate's election agent. Kent Police began an investigation into the spending returns of Mackinlay following the Channel 4 report.[25]

In a court case on 1 June 2016, brought by Mackinlay and his election agent Nathan Gray,[26] District Judge Barron granted more time for investigation saying "In this case, the allegations are far-reaching and the consequences of a conviction would be of a local and national significance with the potential for election results being declared void."[27]

On 14 March 2017, it was reported that Mackinlay had been interviewed under caution by officers investigating the allegations.[28] The day after, Channel 4 News published leaked emails, alleging that Theresa May's Political Secretary Stephen Parkinson, and Chris Brannigan, Director of Government Relations at the Cabinet Office, also took a key role in Mackinlay's campaign.[29] On 18 April 2017, Kent police passed Mackinlay's file to the Crown Prosecution Service to be considered for prosecution.[30] The CPS decided on 2 June 2017 that it was in the public interest to authorise charges under the Representation of the People Act 1983 against three people: Mackinlay, his agent Nathan Gray, and a party activist, Marion Little.[31][32] Appearing at Westminster Magistrates' Court on 4 July 2017, the three pleaded not guilty and were released on unconditional bail pending an appearance at Southwark Crown Court on 1 August 2017.[33][34] Later in August 2017, a trial date of 14 May 2018 was set for Mackinlay on charges relating to his 2015 general election expenses, alongside Little and Gray.[35] The trial eventually started on 15 October 2018.[36] Gray was acquitted in December 2018,[37] and Mackinlay was acquitted on 9 January 2019.[38] Little was convicted of two counts relating to falsifying election expenses, she was given a nine month suspended prison sentence and fined £5,000;[39] the court concluded that Mackinlay and Gray had signed documents falsified by Little "in good faith, not knowing what she had done".[40]

^Daniel, Mark (2005). Cranks and Gadflies: The Story of UKIP. Oxford: Timewell Press. p. 11. ISBN1-85-725209-8. he had no interest in politics until he observed at close quarters the effects of Britain's short lived and ill-fated membership of the EU's Exchange Rate Mechanism.

^Daniel, Mark (2005). Cranks and Gadflies: The Story of UKIP. Oxford: Timewell Press. p. 11. ISBN1-85-725209-8. He heard Sked on a BBC politics programme, telephoned and attended a meeting at the LSE. He too was dragooned into standing for the 1992 election.

^ abcDaniel, Mark (2005). Cranks and Gadflies: The Story of UKIP. Oxford: Timewell Press. pp. 48–51. ISBN1-85-725209-8. he resigned the party leadership, naming Craig Mackinlay as his successor... Holmes accepted the leadership and immediately appointed Mackinlay as his deputy

^"Medway councillor resigns over conflict of interest". BBC News. 28 August 2010. Retrieved 25 June 2012. Councillor Craig Mackinlay, who also represents the River Ward, said there were no regulations preventing special constables from serving on the council and said he knew of three who are serving MPs.